November 5, 2014
Last night, I submitted a paper for publication — for the first time since April 2013. I’d almost forgotten what it felt like. But, because we’re living in the Shiny Digital Future, you don’t have to wait till it’s been through review and formal publication to read it. I submitted to PeerJ, and at the same time, made it available as a preprint (Taylor 2014).
It’s called “Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs”, and frankly the results are weird. Here’s a taste:
A year back, as I was composing a blog-post about our neck-cartilage paper in PLOS ONE (Taylor and Wedel 2013c), I found myself writing down the rather trivial formula for the additional angle of extension at an intervertebral joint once the cartilage is taken into account. In that post, I finished with the promise “I guess that will have to go in a followup now”. Amazingly it’s taken me a year to get that one-pager written and submitted. (Although in the usual way of things, the manuscript ended up being 13 pages long.)
To summarise the main point of the paper: when you insert cartilage of thickness t between two vertebrae whose zygapophyses articulate at height h above the centra, the more anterior vertebra is forced upwards by t/h radians. Our best guess for how much cartilage is between the adjacent vertebrae in an Apatosaurus neck is about 10% of centrum length: the image above shows the effect of inserting that much cartilage at each joint.
And yes, it’s weird. But it’s where the data leads me, so I think it would be dishonest not to publish it.
I’ll be interested to see what the reviewers make of this. You are all of course welcome to leave comments on the preprint itself; but because this is going through conventional peer-review straight away (unlike our Barosaurus preprint), there’s no need to offer the kind of detailed and comprehensive comment that several people did with the previous one. Of course feel free if you wish, but I’m not depending on it.
Gilmore Charles W. 1936. Osteology of Apatosaurus, with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175–300 and plates XXI–XXXIV.
Stevens, Kent A., and J. Michael Parrish. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284(5415):798–800. doi:10.1126/science.284.5415.798
Taylor, Michael P., and Mathew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10):e78214. 17 pages. doi:10.1371/journal.pone.0078214
October 29, 2014
Just a quick post today, to refute an incorrect idea about open access that has unfortunately been propagated from time to time. That is the idea that if (say) PLOS were acquired by a barrier-based publisher such as Taylor and Francis, then its papers could be hidden behind paywalls and effectively lost to the world. For example, in Glyn Moody’s article The Open Access Schism, Heather Morrison is quoted as follows:
A major concern about the current move towards CC-BY is that it might allow re-enclosure by companies […] This is a scenario suggested by assistant professor in the School of Information Studies at the University of Ottawa Heather Morrison. As she explains, “There is nothing in the CC BY license that would stop a business from taking all of the works, with attribution, and selling them under a more restrictive license—not only a more restrictive CC-type license (STM’s license is a good indication of what could happen here), but even behind a paywall, then buying out the OA publisher and taking down the OA content.”
This is flatly incorrect.
Reputable open-access publishers not only publish papers on their own sites but also place them in third-party archives, precisely to guard against doomsday scenarios. If (say) PeerJ were made an offer they couldn’t refuse by Elsevier, then the new owners could certainly shut down the PeerJ site; but there’s nothing the could do about the copies of PeerJ articles on PubMed Central, in CLOCKSS and elsewhere. And of course everyone who already has copies of the articles would always be free to distribute them in any way, including posting complete archives on their own websites.
Let’s not accept this kind of scaremongering.
October 28, 2014
It’s nearly two years since Alexander Brown wrote Open access: why academic publishers still add value for the Guardian, in which he listed ways that he feels publishers make a contribution. I wrote a lengthy comment in response — long enough that it got truncated at 5000 characters and I had to post a second comment with the tail end. At the time, I intended to turn that comment into an SV-POW! post, but for some reason I never did. Belatedly, here it is.
I’m a bit nonplussed by this article, in which a publisher lists a lot of important services that they claim to provide, nearly all of which turn out to be either not important at all (if not actively harmful) or provided for free by academics. Let’s go through them one by one, and see how they measure up against the average cost to academia of $5333 per paywalled academic paper.
strong, skilled editors to ensure that research can be universally understood
It is authors who make their work understood. As the author of a dozen published papers myself, I’ve certainly never received any help from an editor to make my work more comprehensible. But even if I had, this would have been done by a handling editor, who is a volunteer academic.
to recognise emerging fields and create new journals
Publisher don’t recognise emerging fields, researchers do. The last thing we need is more journals — there are already far more than anyone can keep track of. The more fruitful trend is the consolidation into a smaller number of more generalist journals, with tools for finding papers relevant to each individual researcher’s interest. (PLOS ONE exemplifies this.)
to build and maintain the brands and reputations of journals.
Journal brands are actively harmful to science. Please stop building and maintaining them.
recruitment and management of editorial review boards
Yes — this, at last, is a real cost in return for a real benefit.
coordination of peer review to ensure the integrity of the scholarly record
This is done by volunteer academics at no cost to the publisher.
Yes, editorial board members and reviewers are by and large unpaid. However there are still scores of people whose full time jobs are managing this process for a growing body of scientific literature.
This seems more like confession of inefficiency than a claim of achievement. No doubt Google could double the number of managers they have to look after their engineers; but that would hardly result in doubling their output. The real question here should be why traditional publishers feel they need so many staff to do so little.
helping customers learn how best to find what they need
How does this happen? I have never had a publisher help me to find anything.
rigorous efforts to acquire content
This means sending spam emails inviting researchers to submit to journals. Like everyone else I know, I bin these on receipt. Researchers know what journals they want to publish in, and when they discover new journals it’s by word of mouth from trusted colleagues.
publicise the brilliance of our authors
Please. This never happens. Authors need to publicise their own work, with or without the help of their institutions, but certainly without significant help from publishers. Often the publisher’s most significant contribution to the publicity process is to release a paper prematurely, thus destroying any attempt at co-ordinating press embargoes.
Developing systems and platforms that can cost well into the tens of millions of dollars/pounds/euros
Again, the fact that a publisher spends this much only shows how inefficient they are. There are several free journal-management systems, including Annotum (used by PLOS Currents) and Open Journal Systems (used by 11,500 journals). If publishers don’t use these tools, that’s no reason to charge researchers more.
with the advent of mobile technology, the job becomes exponentially more difficult as we add “whenever they want it” to the list of our customers’ needs
I have no idea what this means. Any open-access journal’s article are always free “whenever they want it”, whatever device someone is reading on.
While the dissemination of research may not require ink and paper like it used to, distribution remains a very real cost
Yes. To pick a well-known large-scale example, it costs arXiv about $7 per paper to accept, host, archive and serve each of its papers indefinitely. A bit less than $5333, admittedly.
Also included in these activities are archive projects like the Springer Book Archives, a massive undertaking to digitise more than 150 years of previously unavailable titles
This is indeed a valuable programme. But it has nothing to do with ongoing publishing, and is a red herring in the current discussion.
for OA authors Springer deposits a researcher’s work into the institutional repositories these scientists are often required to use, helping to provide further access to scholarly works.
This is good. It saves the author a good fifteen minutes. £5333 well spent!
It is hard to imagine how anyone with an internet connection could do this with the speed, efficiency and added value with which publishers operate
On the contrary: it’s hard to understand how publishers manage to do it so inefficiently.
I just find all this baffling. Any researcher who has actually been through the process of publication knows that it is researchers who do all the significiant work: not only the research, but the writing, the preparation of illustrations, the editorial process, the peer-reviewing, the copy-editing, and increasingly even the typesetting. Hosting, archiving and replication can be done for $7 per paper. So I still don’t see where the publishers are adding any value that is of value to the academy.
September 18, 2014
There is little enthusiasm for CC-BY […] in the field of political studies. […] It is clear that there is serious concern about the potential for work published under a CC-BY licence to be distorted and used inappropriately.
There may be concern, but it’s misplaced. Using CC By does not allow your work to be misrepresented. The human-readably summary of the licence clearly states, in its definition of the attribution clause: [Emphasis added]
You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
What does this mean? It means creationists can’t take our paper on sauropod neck anatomy, change it so that we seem to be advocating Intelligent Design, and post the result as though it’s our work. Instead, the terms of the licence require that they state that changes were made, and that they do not portray us as endorsing their use.
Really, I don’t see how much clearer or simpler the CC By licence could be. It’s 108 words long. For heavens’ sake, folks, go and read it. It’s ridiculous that we have academics, who are supposed to be trained in research and rigour, expressing flagrantly incorrect opinions about a hundred-word-long document that they’ve not even read.
September 2, 2014
A couple of weeks ago, more than hundred scientists sent an open letter to the AAAS (American Association for the Advancement of Science) about their new open-access journal Science Advances, which is deficient in various ways — not least the absurdly inflated article-processing charge.
Today I learn from email that there has finally been a response — of sorts. Editor-in-Chief Marcia McNutt had a long phone-call with Jon Tennant — one of the hundred-plus authors/co-signers. All we know about that call is (and I quote from Jon’s email account) “it became quite apparent that we would have to agree to disagree on many points”.
All I want to say is this. When a hundred scientists co-sign an open letter, it is TOTALLY UNACCEPTABLE for the response to take the form of a private telephone call with one of those authors.
Come on, AAAS. This is all about openness. Let’s see an open response: a substantive, non-patronising one which addresses the actual points made in the original letter.
Meanwhile, you may like to read this article at The New Statesman: Scientists criticise new “open access” journal which limits research-sharing with copyright. In finishes on this very clear note, courtesy of Jon Tennant:
The AAAS should be a shining beacon within the academic world for progression of science. If this is their best shot at that, it’s an absolute disaster at the start on all levels. What publishers need to remember is that the academic community is not here to serve them – it is the other way around.
August 15, 2014
This is an open letter concerning the recent launch of the new open access journal, Science Advances. In addition to the welcome diversification in journal choices for authors looking for open access venues, there are many positive aspects of Science Advances: its broad STEM scope, its interest in cross-disciplinary research, and the offering of fee waivers. While we welcome the commitment of the Association to open access, we are also deeply concerned with the specific approach. Herein, we outline a number of suggestions that are in line with both the current direction that scholarly publishing is taking and the needs expressed by the open access community, which this journal aims to serve.
The first of these issues concerns the licensing terms of the journal articles. The default choice of a non-commercial licence (CC BY-NC) places unnecessary restrictions on reuse and does not meet the standards set out by the Budapest Open Access Initiative. Many large funders, including Research Councils UK and the Wellcome Trust, do not recognise this as an open license. The adoption of CC BY-NC as the default license means that many researchers will be unable to submit to Science Advances if they are to conform to their funder mandates unless they pay for the upgrade to CC BY. There is little evidence that non-commercial restrictions provide a benefit to the progress of scholarly research, yet they have significant negative impact, limiting the ability to reuse material for educational purposes and advocacy. For example, NC-encumbered materials cannot be used on Wikipedia. The non-commercial clause is known to generate ambiguities and uncertainties (see for example, NC Licenses Considered Harmful) to the detriment of scholarly communication. Additionally, there is little robust evidence to suggest that adopting a CC-BY license will lead to income loss for your Association, and the $1,000 surcharge is difficult to justify or defend. The value of the CC BY license is outlined in detail by the Open Access Scholarly Publishers Association.
We raise an additional issue with the $1,500 surcharge for articles more than 10 pages in length. In an online-only format, page length is an arbitrary unit that results from the article being read in PDF format. Can the AAAS explain what the additional costs associated with the increased length are that would warrant a 50% increase in APC for an unspecified number of additional digital pages? Other leading open access journals, such as PeerJ, the BMC series, and PLOS ONE, offer publication of articles with unlimited page lengths. The extra costs create constraints that may adversely incentivize authors to exclude important details of their study, preventing replication and hindering transparency, all of which are contrary to the aims of scholarly publication. Therefore it seems counterproductive to impose this additional charge; it discriminates against researchers’ best effort to communicate their findings with as much detail as necessary.
We feel that the proposed APCs and licencing scheme are detrimental to the AAAS and the global academic community. As such, we recommend that Science Advances:
Offers CC BY as standard for no additional cost, in line with leading open access publishers, so authors are able to comply with respective funding mandates;
Provides a transparent calculation of its APCs based on the publishing practices of the AAAS and explains how additional value created by the journal will measure against the significantly high prices paid by the authors;
Removes the surcharges associated with increased page number;
We hope that you will consider the points raised above, keeping in mind how best to serve the scientific community, and use Science Advances to add the AAAS to the group of progressive and innovative open access scholarly publishers. We hope AAAS will collaborate with the academic community to facilitate the dissemination of scientific knowledge through a journal committed to fully embracing the principles of Open Access.
We kindly request that you allow your response(s) to be made public along with this letter, and look forward to hearing your response soon.
Signatories (please note that we do not formally represent the institutions listed):
- Jonathan P. Tennant, PhD student, Imperial College London (firstname.lastname@example.org, @protohedgehog)
- Timothée Poisot, University of Canterbury (email@example.com, @tpoi)
- Joseph R. Hancock, Montana State University-Bozeman (firstname.lastname@example.org, @Joe_R_Hancock)
- M Fabiana Kubke, University of Auckland, New Zealand (email@example.com, @kubke)
- François Michonneau, University of Florida (firstname.lastname@example.org, @FrancoisInvert)
- Michael P. Taylor, University of Bristol (email@example.com, @MikeTaylor)
- Graham Steel, Open Science, Scotland (firstname.lastname@example.org, @McDawg)
- Jérémy Anquetin, Section d’Archéologie et Paléontologie, Switzerland (email@example.com, @FossilTurtles)
- Emily Coyte, University of Bristol (firstname.lastname@example.org, @emilycoyte)
- Benjamin Schwessinger, UC Davis (email@example.com, @schwessinger)
- Erin C. McKiernan, independent scientist (firstname.lastname@example.org, @emckiernan13)
- Tom Pollard, PhD student, University College London (email@example.com, @tompollard)
- Aimee Eckert, MRes student, Imperial College London (firstname.lastname@example.org, @aimee_e27)
- Liz Allen, ScienceOpen, San Francisco (email@example.com, @LizAllenSO)
- Dalmeet Singh Chawla, Imperial College London (firstname.lastname@example.org, @DalmeetS)
- Elizabeth Silva, San Francisco (email@example.com, @lizatucsf)
- Nicholas Gardner, Marshall University (firstname.lastname@example.org, @RomerianReptile)
- Nathan Cantley, Medical Student, Queens University Belfast (email@example.com, @NathanWPCantley)
- John Dupuis, Librarian, York University, Toronto (firstname.lastname@example.org, @dupuisj)
- Christina Pikas, Doctoral Candidate, University of Maryland (email@example.com, @cpikas)
- Amy Buckland, Librarian, McGill University, Montreal (firstname.lastname@example.org, @jambina)
- Lenny Teytelman, www.zappylab.com, Berkeley, CA (email@example.com), @lteytelman)
- Peter Murray-Rust, University of Cambridge, UK (firstname.lastname@example.org), @petermurrayrust)
- Zen Faulkes, The University of Texas-Pan American, email@example.com, @DoctorZen)
- Robert J. Gay, The University of Arizona/Mission Heights Preparatory High School, AZ, USA (firstname.lastname@example.org, @paleorob)
- Peter T.B. Brett, University of Surrey, UK (email@example.com, @PeterTBBrett)
- Anders Eklund, Linköping University, Sweden (firstname.lastname@example.org, @wandedob)
- Johannes Björk, Institute of Marine Sciences, Barcelona, Spain (email@example.com, @AwfulDodger)
- William Gunn, Mendeley, London, UK, firstname.lastname@example.org, @mrgunn)
- Nitika Pant Pai, McGill University, Montreal, Canada (email@example.com) @nikkiannike
- Philippe Desjardins-Proulx, Ph.D. student (firstname.lastname@example.org, @phdpqc).
- Joshua M. Nicholson, PhD candidate Virginia Tech, VA and founder The Winnower, VA (email@example.com, @thewinnower)
- Scott Edmunds, GigaScience, BGI Hong Kong (firstname.lastname@example.org, @SCEdmunds)
- Steven Ray Wilson, University of Oslo (email@example.com, @stevenRayOslo)
- Stuart Buck, Vice President of Research Integrity, Laura and John Arnold Foundation (firstname.lastname@example.org, @stuartbuck1)
- B. Arman Aksoy, Ph.D. student, Memorial Sloan Kettering Cancer Center (email@example.com, @armish)
- Nazeefa Fatima, University of Huddersfield, UK (firstname.lastname@example.org, @NazeefaFatima)
- Ross Mounce, University of Bath, UK (email@example.com, @rmounce)
- Heather Piwowar, Impactstory, (firstname.lastname@example.org), @researchremix
- Avinash Thirumalai, Ph.D student, East Tennessee State University (email@example.com)
- Jason Priem, Impactstory (firstname.lastname@example.org), @jasonpriem
- Clayton Aldern, University of Oxford, UK (email@example.com, @compatibilism)
- Marcus D. Hanwell, Technical Leader, Kitware, Inc., (firstname.lastname@example.org, @mhanwell)
- Kristen L. Marhaver, NSF Postdoctoral Fellow, Carmabi Foundation (email@example.com, @CoralSci)
- David Michael Roberts, ARC Research Associate, University of Adelaide (firstname.lastname@example.org)
- Brian Hole, Ubiquity Press, UK (email@example.com, @ubiquitypress)
- Alexander Grossmann, University of Applied Sciences Leipzig, Germany and co-founder of ScienceOpen, Berlin/Boston (firstname.lastname@example.org, @SciPubLab)
- David L.Vaux, Assistant Director, The Walter and Eliza Hall Institute, Australia (email@example.com)
- John Murtagh, Repository Manager, London School of Hygiene and Tropical Medicine @LSHTMlibrary
- Alecia Carter, University of Cambridge, UK (firstname.lastname@example.org, @alecia_carter)
- Alex O. Holcombe, University of Sydney (email@example.com, @ceptional)
- Ignacio Torres Aleman, Cajal Institute, Madrid. Spain. (firstname.lastname@example.org)
- Sarah Molloy, Research Support Manager, Queen Mary University of London (email@example.com, @moragm23)
- John Lamp, Deakin University, Australia (firstname.lastname@example.org, @johnwlamp)
- Matthew Todd, The University of Sydney and Open Source Malaria, email@example.com)
- Anusha Seneviratne, Imperial College London (firstname.lastname@example.org, @anushans)
- Guido Guidotti, Harvard University (email@example.com)
- Joseph McArthur, Assistant Director, Right to Research Coalition(Joe@RighttoResearch.org, @mcarthur_joe)
- Carlos H. Grohmann, University of São Paulo, Brazil (firstname.lastname@example.org)
- Jan de Leeuw, University of California Los Angeles, (email@example.com)
- Jung H. Choi, Associate Professor, Georgia Institute of Technology (firstname.lastname@example.org)
- Ernesto Priego, Centre for Information Science, City University London, UK (Ernesto.Priego.email@example.com)
- Brian Pasley, University of California, Berkeley (firstname.lastname@example.org)
- Stacy Konkiel, Impactstory.org (email@example.com), @skonkiel)
- Elizabeth HB Hellen, Rutgers University (firstname.lastname@example.org)
- Raphael Levy, University of Liverpool (email@example.com)
- Paul Coxon, University of Cambridge (firstname.lastname@example.org)
- Nitika Pant Pai, McGill University, Montreal, Canada (email@example.com)
- David Carroll, Queen’s University Belfast (firstname.lastname@example.org, @davidecarroll)
- Jacinto Dávila, Universidad de Los Andes (email@example.com, @jacintodavila)
- Marco Arieli Herrera-Valdez, Universidad Nacional Autónoma de México (firstname.lastname@example.org, @brujonildo)
- Juan Pablo Alperin, Simon Fraser University, Canada (email@example.com)
- Jan P. de Ruiter, Bielefeld University (firstname.lastname@example.org, @JPdeRuiter)
- Xianwen Chen, Norwegian University of Life Sciences (email@example.com, @xianwen_chen)
- Jeanette Hatherill, Librarian, University of Ottawa, Canada (firstname.lastname@example.org, @jeanetteanneh)
- Katharine Mullen, University of California Los Angeles (email@example.com)
- Pedro Bekinschtein, University of Buenos Aires, Argentina (firstname.lastname@example.org; @pedrobek)
- Quentin Groom, Botanic Garden Meise, Belgium (email@example.com, @cabbageleek)
- Karen Meijer-Kline, Librarian, Simon Fraser University, Canada (firstname.lastname@example.org, @kmeijerkline)
- Pietro Gatti-Lafranconi, Department of Biochemistry, University of Cambridge, UK (email@example.com, @p_gl)
- Jeffrey Hollister, USEPA, Narragansett, RI (firstname.lastname@example.org, @jhollist)
- Lachlan Coin, University of Queensland and founder of Academic Karma (email@example.com @AcademicKarma )
- MooYoung Choi, Department of Physics and Astronomy, Seoul National University, Korea (firstname.lastname@example.org)
- Oscar Patterson-Lomba, Harvard School of Public Health (email@example.com)
- Rowena Ball, The Australian National University, Canberra, Australia (Rowena.Ball@anu.edu.au)
- Daniel Swan, Oxford Gene Technology, UK (Daniel.Swan@ogt.com @DrDanielSwan)
- Stephen Curry, Imperial College London, UK (firstname.lastname@example.org, @Stephen_Curry)
- Abigail Noyce, Boston University (email@example.com, @abbynoyce)
- Jordan Ward, UCSF, San Francisco, CA, USA (firstname.lastname@example.org, @Jordan_D_Ward)
- Ben Meghreblian, criticalscience.com, London, UK (email@example.com, @benmeg)
- Ethan P. White, Utah State University, Logan, UT, USA (firstname.lastname@example.org, @ethanwhite)
- Sean R. Mulcahy, University of California, Berkeley, CA, USA (email@example.com, @srmulcahy)
- Sibele Fausto, University of São Paulo, Brazil (firstname.lastname@example.org @sibelefausto)
- Lorena A. Barba, George Washington University (email@example.com @LorenaABarba)
- Ed Trollope, Director, Things We Don’t Know CIC (firstname.lastname@example.org, @TWeDK)
- Stephen Beckett, Ph.D. student, University of Exeter (S.J.Beckett@exeter.ac.uk, @BeckettStephen)
- Andrew D. Steen, Department of Earth & Planetary Sciences, University of Tennessee, Knoxville (email@example.com, @drdrewsteen)
- Mari Sarv, Estonian Literary Museum (firstname.lastname@example.org, @kaskekanke)
- Noam Ross, Ph.D. Candidate, Ecology, University of California-Davis (email@example.com, @noamross)
- Erika Amir, Geologist, Massachusetts, USA (firstname.lastname@example.org, @geoflier)
- Martin Paul Eve, University of Lincoln (email@example.com, @martin_eve)
- Franco Cecchi, University of Florence (firstname.lastname@example.org)
- Jason B. Colditz, University of Pittsburgh (email@example.com, @colditzjb)
- Philip Spear, postdoc, Northwestern University (firstname.lastname@example.org)
- Mythili Menon, University of Southern California (email@example.com, @mythmenon)
- Matthew Clapham, University of California Santa Cruz (firstname.lastname@example.org,@meclapham)
- Karl W. Broman, University of Wisconsin–Madison (email@example.com, @kwbroman)
- Graham Triggs, Symplectic (firstname.lastname@example.org, @grahamtriggs)
- Tom Crick, Cardiff Metropolitan University (email@example.com, @DrTomCrick)
- Diano F. Marrone, Wilfrid Laurier University (firstname.lastname@example.org)
- Joseph Kraus, Librarian, University of Denver (email@example.com, @OAJoe)
- Steven Buyske, Rutgers University (firstname.lastname@example.org)
- Gavin Simpson, University of Regina (email@example.com)
- Colleen Morgan, University of York (firstname.lastname@example.org @clmorgan)
- Kara Woo, National Center for Ecological Analysis and Synthesis, UC Santa Barbara (email@example.com, @kara_woo)
- Mathew Wedel, Western University of Health Sciences (firstname.lastname@example.org)